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<HR>

<H3>1. Introduction 
</H3>
<P>These sections describe what Pizza.py is, what it means to be
open-source software, and acknowledge the funding and people who have
contributed to Pizza.py.
</P>
1.1 <A HREF = "#1_1">What is Pizza.Py</A><BR>
1.2 <A HREF = "#1_2">Open source distribution</A><BR>
1.3 <A HREF = "#1_3">Acknowledgements</A> <BR>

<HR>

<A NAME = "1_1"></A><H4>1.1 What is Pizza.py 
</H4>
<P>Pizza.py is a loosely integrated collection of tools, many of which
provide pre- and post-processing capabilities for the <A HREF = "http://www.cs.sandia.gov/~sjplimp/lammps.html">LAMMPS</A>
molecular dynamics and <A HREF = "http://www.cs.sandia.gov/~sjplimp/chemcell.html">ChemCell</A> cell simulator packages.
</P>




<P>There are tools to create input files, convert between file formats to
connect to other codes, process log and dump files, plot output, and
visualize and animate simulation snapshots.
</P>
<P>Python is used in Pizza.py in 3 ways:
</P>
<UL><LI>to provide an interactive and scripting interface to the tools
<LI>as a language for writing tools
<LI>to wrap existing stand-alone codes 
</UL>
<P>Python makes it easy for users of Pizza.py to:
</P>
<UL><LI>experiment with tools interactively
<LI>automate tasks as script files of commands
<LI>extend tools or create new ones 
</UL>
<P>The topmost level of Pizza.py adds a modest bit of functionality to
the Python interpreter to make it easier to invoke tools and pass data
between them.  As such, Python is an ideal "framework" or "glue"
language that enables various tools to be hooked together, while also
providing a rich programming environment of its own.
</P>
<HR>

<A NAME = "1_2"></A><H4>1.2 Open source distribution 
</H4>
<P>Pizza.py comes with no warranty of any kind.  As each source file
states in its header, it is distributed free-of-charge, under the
terms of the <A HREF = "http://www.gnu.org/copyleft/gpl.html">GNU Public License</A> (GPL).  This is often referred
to as open-source distribution - see <A HREF = "http://www.gnu.org">www.gnu.org</A> or
<A HREF = "http://www.opensource.org">www.opensource.org</A> for more details.  The legal text of
the GPL is in the LICENSE file that is included in the Pizza.py
distribution.
</P>






<P>Here is a summary of what the GPL means for Pizza.py users:
</P>
<P>(1) Anyone is free to use, modify, or extend Pizza.py in any way they
choose, including for commercial purposes.
</P>
<P>(2) If you distribute a modified version of Pizza.py, it must remain
open-source, meaning you distribute it under the terms of the GPL.
You should clearly annotate such a code as a derivative version of
Pizza.py.
</P>
<P>(3) If you release any code that includes Pizza.py source code, then
it must also be open-sourced, meaning you distribute it under the
terms of the GPL.
</P>
<P>(4) If you give Pizza.py to someone else, the GPL LICENSE file and
source file headers (including the GPL notices) should remain part of
the code.
</P>
<P>In the spirit of an open-source code, these are various ways you can
contribute to making Pizza.py better.  You can send email to
sjplimp@sandia.gov on any of these items.
</P>
<UL><LI>If you write a Pizza.py script that is generally useful or illustrates
how to do something cool with Pizza.py, it can be added to the
Pizza.py distribution.  Ditto for a picture or movie that can be added
to the <A HREF = "http://pizza.sandia.gov">Pizza.py WWW site</A>. 

<LI>If you add a new method to one of the tools or create a new tool that
is useful for Pizza.py or LAMMPS or ChemCell users, it can be added to
the Pizza.py distribution.  See the ToDo list at the beginning of the
src/*.py files for features that haven't yet been implemented. 

<LI>If you find a bug, report it. 

<LI>Report if you find an error or omission in the <A HREF = "Manual.html">Pizza.py
documentation</A> or on the <A HREF = "http://pizza.sandia.gov">Pizza.py WWW Site</A>, or have a
suggestion for something to clarify or include. 

<LI>Point prospective users to the <A HREF = "http://pizza.sandia.gov">Pizza.py WWW Site</A> or link to it
from your WWW site. 
</UL>
<HR>

<H4><A NAME = "1_3"></A>1.3 Acknowledgements 
</H4>
<P>Pizza.py has been developed at <A HREF = "http://www.sandia.gov">Sandia National Laboratories</A>
which is a multiprogram laboratory operated by Sandia Corporation, a
Lockheed Martin Company, for the United States Department of Energy's
National Nuclear Security Administration under contract
DE-AC04-94AL85000.
</P>
<P>Funding for Pizza.py development has come from the US Department of
Energy (<A HREF = "http://www.doe.gov">DOE</A>), through its LDRD and Genomes-to-Life programs.
The latter effort has been funded by DOE's <A HREF = "http://www.sc.doe.gov/ascr/home.html">OASCR</A> and
<A HREF = "http://www.er.doe.gov/production/ober/ober_top.html">OBER</A> offices as part of the US Department of Energy's
Genomics:GTL program (<A HREF = "http://www.doegenomestolife.org">www.doegenomestolife.org</A>) under the
<A HREF = "http://www.genomes2life.org">project</A>, "Carbon Sequestration in Synechococcus Sp.: From
Molecular Machines to Hierarchical Modeling".
</P>












<P>The maintainer of Pizza.py is <A HREF = "http://www.cs.sandia.gov/~sjplimp">Steve Plimpton</A>.
</P>


<P>Matt Jones, a BYU student who was a summer intern at Sandia, wrote
several of the coolest tools in Pizza.py and about half the code in
the initial version.
</P>
<P>Others who have written tools or scripts that are part of the Pizza.py
distribution are listed on the <A HREF = "http://www.cs.sandia.gov/~sjplimp/pizza/thanks.html">Pizza.py WWW site</A>.
</P>


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